X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=c8ab7ba8dc2535940ca6b30fe43d0d2206207594;hb=dda27af89b70c52e075f6531d56c0bbccbc7246d;hp=ee49cd3cff69afb2c0872978293fd3eaf0e13d9c;hpb=e23eb12b5f2c9b50b7db68b9aa972e50155540eb;p=samtools.git diff --git a/bam_plcmd.c b/bam_plcmd.c index ee49cd3..c8ab7ba 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -5,7 +5,6 @@ #include "sam.h" #include "faidx.h" #include "bam_maqcns.h" -#include "bam_mcns.h" #include "khash.h" #include "glf.h" #include "kstring.h" @@ -342,12 +341,12 @@ int bam_pileup(int argc, char *argv[]) d->max_depth = 0; d->tid = -1; d->mask = BAM_DEF_MASK; d->c = bam_maqcns_init(); - d->c->is_soap = 1; // change the default model + d->c->errmod = BAM_ERRMOD_MAQ2; // change the default model d->ido = bam_maqindel_opt_init(); while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PA")) >= 0) { switch (c) { - case 'a': d->c->is_soap = 1; break; - case 'A': d->c->is_soap = 0; break; + case 'a': d->c->errmod = BAM_ERRMOD_SOAP; break; + case 'A': d->c->errmod = BAM_ERRMOD_MAQ; break; case 's': d->format |= BAM_PLF_SIMPLE; break; case 't': fn_list = strdup(optarg); break; case 'l': fn_pos = strdup(optarg); break; @@ -376,6 +375,8 @@ int bam_pileup(int argc, char *argv[]) default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1; } } + if (d->c->errmod != BAM_ERRMOD_MAQ2) d->c->theta += 0.02; + if (d->c->theta > 1.0) d->c->theta = 1.0; if (fn_list) is_SAM = 1; if (optind == argc) { fprintf(stderr, "\n"); @@ -449,9 +450,17 @@ int bam_pileup(int argc, char *argv[]) * mpileup * ***********/ +#include +#include "bam2bcf.h" +#include "sample.h" + +#define MPLP_GLF 0x10 +#define MPLP_NO_COMP 0x20 +#define MPLP_NO_ORPHAN 0x40 +#define MPLP_REALN 0x80 + typedef struct { - int vcf, max_mq, min_mq, var_only, prior_type, afs; - double theta; + int max_mq, min_mq, flag, min_baseQ, capQ_thres; char *reg, *fn_pos; faidx_t *fai; kh_64_t *hash; @@ -460,40 +469,101 @@ typedef struct { typedef struct { bamFile fp; bam_iter_t iter; - int min_mq; + int min_mq, flag, ref_id, capQ_thres; + char *ref; } mplp_aux_t; +typedef struct { + int n; + int *n_plp, *m_plp; + bam_pileup1_t **plp; +} mplp_pileup_t; + static int mplp_func(void *data, bam1_t *b) { + extern int bam_realn(bam1_t *b, const char *ref); + extern int bam_prob_realn(bam1_t *b, const char *ref); + extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres); mplp_aux_t *ma = (mplp_aux_t*)data; - int ret; + int ret, skip = 0; do { + int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b); - } while (b->core.qual < ma->min_mq && ret >= 0); + if (ret < 0) break; + skip = 0; + if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn(b, ma->ref); + if (has_ref && ma->capQ_thres > 10) { + int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres); + if (q < 0) skip = 1; + else if (b->core.qual > q) b->core.qual = q; + } else if (b->core.flag&BAM_FUNMAP) skip = 1; + else if (b->core.qual < ma->min_mq) skip = 1; + else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1; + } while (skip); return ret; } +static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf, + int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp) +{ + int i, j; + memset(m->n_plp, 0, m->n * sizeof(int)); + for (i = 0; i < n; ++i) { + for (j = 0; j < n_plp[i]; ++j) { + const bam_pileup1_t *p = plp[i] + j; + uint8_t *q; + int id = -1; + q = bam_aux_get(p->b, "RG"); + if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf); + if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf); + assert(id >= 0 && id < m->n); + if (m->n_plp[id] == m->m_plp[id]) { + m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8; + m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]); + } + m->plp[id][m->n_plp[id]++] = *p; + } + } +} + static int mpileup(mplp_conf_t *conf, int n, char **fn) { mplp_aux_t **data; - mc_aux_t *ma = 0; int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid; const bam_pileup1_t **plp; bam_mplp_t iter; bam_header_t *h = 0; char *ref; khash_t(64) *hash = 0; - // allocate + + bcf_callaux_t *bca = 0; + bcf_callret1_t *bcr = 0; + bcf_call_t bc; + bcf_t *bp = 0; + bcf_hdr_t *bh = 0; + + bam_sample_t *sm = 0; + kstring_t buf; + mplp_pileup_t gplp; + + memset(&gplp, 0, sizeof(mplp_pileup_t)); + memset(&buf, 0, sizeof(kstring_t)); + memset(&bc, 0, sizeof(bcf_call_t)); data = calloc(n, sizeof(void*)); plp = calloc(n, sizeof(void*)); n_plp = calloc(n, sizeof(int*)); + sm = bam_smpl_init(); + // read the header and initialize data for (i = 0; i < n; ++i) { bam_header_t *h_tmp; data[i] = calloc(1, sizeof(mplp_aux_t)); data[i]->min_mq = conf->min_mq; - data[i]->fp = bam_open(fn[i], "r"); + data[i]->flag = conf->flag; + data[i]->capQ_thres = conf->capQ_thres; + data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r"); h_tmp = bam_header_read(data[i]->fp); + bam_smpl_add(sm, fn[i], h_tmp->text); if (conf->reg) { int beg, end; bam_index_t *idx; @@ -516,31 +586,39 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) bam_header_destroy(h_tmp); } } + gplp.n = sm->n; + gplp.n_plp = calloc(sm->n, sizeof(int)); + gplp.m_plp = calloc(sm->n, sizeof(int)); + gplp.plp = calloc(sm->n, sizeof(void*)); + + fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n); if (conf->fn_pos) hash = load_pos(conf->fn_pos, h); // write the VCF header - if (conf->vcf) { + if (conf->flag & MPLP_GLF) { kstring_t s; + bh = calloc(1, sizeof(bcf_hdr_t)); s.l = s.m = 0; s.s = 0; - puts("##fileformat=VCFv4.0"); - puts("##INFO="); -// puts("##INFO="); -// puts("##INFO="); - puts("##FILTER="); - kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s); - for (i = 0; i < n; ++i) { - const char *p; - kputc('\t', &s); - if ((p = strstr(fn[i], ".bam")) != 0) - kputsn(fn[i], p - fn[i], &s); - else kputs(fn[i], &s); + bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w"); + for (i = 0; i < h->n_targets; ++i) { + kputs(h->target_name[i], &s); + kputc('\0', &s); + } + bh->l_nm = s.l; + bh->name = malloc(s.l); + memcpy(bh->name, s.s, s.l); + s.l = 0; + for (i = 0; i < sm->n; ++i) { + kputs(sm->smpl[i], &s); kputc('\0', &s); } - puts(s.s); + bh->l_smpl = s.l; + bh->sname = malloc(s.l); + memcpy(bh->sname, s.s, s.l); + bh->l_txt = 0; free(s.s); - } - // mpileup - if (conf->vcf) { - ma = mc_init(n); - mc_init_prior(ma, conf->prior_type, conf->theta); + bcf_hdr_sync(bh); + bcf_hdr_write(bp, bh); + bca = bcf_call_init(-1., conf->min_baseQ); + bcr = calloc(sm->n, sizeof(bcf_callret1_t)); } ref_tid = -1; ref = 0; iter = bam_mplp_init(n, mplp_func, (void**)data); @@ -552,56 +630,23 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) if (k == kh_end(hash)) continue; } if (tid != ref_tid) { - free(ref); + free(ref); ref = 0; if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len); + for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid; ref_tid = tid; } - if (conf->vcf) { - mc_rst_t r; - int j, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0, level = 2, tot; - uint64_t sqr_sum; - if (conf->afs) level = 3; - _ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N'; - _ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]]; - tot = mc_cal(_ref0, n_plp, plp, ma, &r, level); - if (tot) { // has good bases - double q; - is_var = (r.p_ref < .5); - q = is_var? r.p_ref : 1. - r.p_ref; - if (q < 1e-308) q = 1e-308; - qref = (int)(-3.434 * log(q) + .499); - if (qref > 99) qref = 99; - } - if (conf->var_only && !is_var) continue; - printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, _ref0b); - if (is_var) { - if (_ref0 == r.ref) putchar("ACGTN"[r.alt]); - else printf("%c,%c", "ACGTN"[r.ref], "ACGTN"[r.alt]); - } else putchar('.'); - printf("\t%d\t", qref); - if (!tot) printf("Q13\t"); - else printf(".\t"); - for (i = depth = 0, sqr_sum = 0; i < n; ++i) { - depth += n_plp[i]; - for (j = 0; j < n_plp[i]; ++j) { - int q = plp[i][j].b->core.qual; - if (q > conf->max_mq) q = conf->max_mq; - sqr_sum += q * q; - } - } - rms_q = (int)(sqrt((double)sqr_sum / depth) + .499); - printf("DP=%d;MQ=%d", depth, rms_q); - printf(";AF=%.3lg", 1. - r.f_em); - if (conf->afs) - printf(";AF0=%.3lg;AFN=%.3lg;AFE=%.3lg", 1-r.f_naive, 1-r.f_nielsen, 1-r.f_exp); - printf("\tGT:GQ:DP"); - if (tot) { - for (i = 0; i < n; ++i) { - int x = mc_call_gt(ma, r.f_em, i); - printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]); - } - } else for (i = 0; i < n; ++i) printf("\t./.:0:0"); - putchar('\n'); + if (conf->flag & MPLP_GLF) { + int _ref0, ref16; + bcf1_t *b = calloc(1, sizeof(bcf1_t)); + group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp); + _ref0 = (ref && pos < ref_len)? ref[pos] : 'N'; + ref16 = bam_nt16_table[_ref0]; + for (i = 0; i < gplp.n; ++i) + bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); + bcf_call_combine(gplp.n, bcr, ref16, &bc); + bcf_call2bcf(tid, pos, &bc, b); + bcf_write(bp, bh, b); + bcf_destroy(b); } else { printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N'); for (i = 0; i < n; ++i) { @@ -623,13 +668,18 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) putchar('\n'); } } + + bcf_close(bp); + bam_smpl_destroy(sm); free(buf.s); + for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); + free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp); if (hash) { // free the hash table khint_t k; for (k = kh_begin(hash); k < kh_end(hash); ++k) if (kh_exist(hash, k)) free(kh_val(hash, k)); kh_destroy(64, hash); } - mc_destroy(ma); + bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr); bam_mplp_destroy(iter); bam_header_destroy(h); for (i = 0; i < n; ++i) { @@ -647,23 +697,25 @@ int bam_mpileup(int argc, char *argv[]) mplp_conf_t mplp; memset(&mplp, 0, sizeof(mplp_conf_t)); mplp.max_mq = 60; - mplp.prior_type = MC_PTYPE_FULL; - mplp.theta = 1e-3; - while ((c = getopt(argc, argv, "f:r:l:VvM:q:t:2F")) >= 0) { + mplp.min_baseQ = 13; + mplp.capQ_thres = 0; + while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) { switch (c) { - case 't': mplp.theta = atof(optarg); break; - case '2': mplp.prior_type = MC_PTYPE_COND2; break; case 'f': mplp.fai = fai_load(optarg); if (mplp.fai == 0) return 1; break; case 'r': mplp.reg = strdup(optarg); break; case 'l': mplp.fn_pos = strdup(optarg); break; - case 'v': mplp.var_only = 1; break; - case 'V': mplp.vcf = 1; break; + case 'g': mplp.flag |= MPLP_GLF; break; + case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break; + case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break; + case 'O': mplp.flag |= MPLP_NO_ORPHAN; break; + case 'R': mplp.flag |= MPLP_REALN; break; + case 'C': mplp.capQ_thres = atoi(optarg); break; case 'M': mplp.max_mq = atoi(optarg); break; case 'q': mplp.min_mq = atoi(optarg); break; - case 'F': mplp.afs = 1; break; + case 'Q': mplp.min_baseQ = atoi(optarg); break; } } if (argc == 1) { @@ -673,13 +725,12 @@ int bam_mpileup(int argc, char *argv[]) fprintf(stderr, " -r STR region in which pileup is generated [null]\n"); fprintf(stderr, " -l FILE list of positions (format: chr pos) [null]\n"); fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq); + fprintf(stderr, " -Q INT min base quality [%d]\n", mplp.min_baseQ); fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq); - fprintf(stderr, " -t FLOAT scaled mutation rate [%lg]\n", mplp.theta); - fprintf(stderr, " -V generate VCF output (SNP calling)\n"); - fprintf(stderr, " -v show variant sites only\n"); - fprintf(stderr, " -2 conditional prior\n"); + fprintf(stderr, " -g generate BCF output\n"); + fprintf(stderr, " -u do not compress BCF output\n"); fprintf(stderr, "\n"); - fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n"); + fprintf(stderr, "Notes: Assuming diploid individuals.\n\n"); return 1; } mpileup(&mplp, argc - optind, argv + optind);